Research workbench
Trypanosoma brucei PTR1 in complex with inhibitor F032
Analyse Trypanosoma brucei PTR1 in complex with inhibitor F032 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IZC
- Type
- protein
- Length
- 985 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- EC
- 1.5.1.33
- UniProt
- O76290
- Ligands
- NAP, 6F4
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase (EC 1.5.1.33) | protein | 249 | 48% helix, 15% strand | O76290 |
| B | Pteridine reductase (EC 1.5.1.33) | protein | 247 | 47% helix, 15% strand | O76290 |
| C | Pteridine reductase (EC 1.5.1.33) | protein | 241 | 46% helix, 15% strand | O76290 |
| D | Pteridine reductase (EC 1.5.1.33) | protein | 248 | 49% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 6F4 · N~2~-[(thiophen-2-yl)methyl]-1,3,4-thiadiazole-2,5-diamine · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 3 copies · chains A, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.84 | 0.85 | 68 | empty |
| 2 | 603 | 0.78 | 0.84 | 46 | NAP, 6F4 |
| 3 | 610 | 0.78 | 0.83 | 48 | NAP, 6F4 |
| 4 | 579 | 0.77 | 0.83 | 45 | NAP, 6F4 |
| 5 | 543 | 0.76 | 0.83 | 44 | NAP, 6F4 |
Interfaces
6 interfaces between chains.
- B–D · 1822 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1819 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1426 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1403 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 566 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (artifact, oxidation).
Compared structures
- 5IZC · Trypanosoma brucei PTR1 in complex with inhibitor F032 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O76290
- Elsewhere: RCSB PDB 5IZC · PDBe 5IZC · UniProt O76290
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